March 10, 2009

In reading up on Obama’s stem cell decision, I got confused about what exactly it does. This line, in particular, confused me (from the WSJ):

The new policy won't affect federal laws that prevent the use of federal money to destroy human embryos. So while it will substantially broaden research opportunities on established cell lines, it won't allow the creation of new ones.

Huh? Wasn’t that Bush’s policy too? This may be common knowledge to everyone but me. But just in case anyone else was confused, here’s a basic rundown of legal landscape (most details come from this CRS report, via the most awesome OpenCRS):

In 1996, Congress passed the Dickey Amendment, which prohibits federal funds from being used to destroy embryos (which is of course what happens when you remove stem cells). In 1999, Clinton’s HHS got around this ban by interpreting “embryo” as excluding already-created embryonic stem cells.

The upshot was that while federal funds could be used for embryonic stem cell research, they couldn’t be used to obtain those cells in the first place. My guess, though, is that most labs could do some fancy accounting (e.g., making sure extraction is covered by “non-federal” funds), and conduct as much research as they wanted.

Congressional Republicans, however, weren’t exactly thrilled with the HHS interpretation. And so when the Decider retreated to a Zen-like meditative state to contemplate these weighty issues, he came up with a “compromise.” Bush allowed funding for a few cell lines that had already been created. But he banned funding for any stem cell lines created after August 2001. He claimed there were about 60 lines at the time, but 58 of those turned out to be bread mold I think.

Anyway, that’s what Obama’s order presumably will do – the federal government will be able to fund research on any already-created stem cell lines, regardless of when they were created. Maybe science wonks can jump in – but that’s probably all that research labs need. The Dickey Amendment doesn’t seem like a big obstacle to me.

That said, it’s still probably worth getting rid of the Dickey Amendment at some point (or at least rewording it), even if it doesn’t pose a research obstacle. The problem with leaving the definition in the hands of the executive branch is that Republicans will control the White House again one day. If Governor Palin wins in 2012 (with an assist from Citigroup), the ban is back on.

So the Democrats should eventually – maybe not in the middle of the current economic battle – get around to amending that statute while they have such strong majorities. Once enacted, Republicans would have to break a filibuster to change the definition, and life-saving research would be more safe.

February 15, 2009

"Some ant species do not have queen ants in the strict sense. Instead, worker ants (which are all female) that have mated with a male ant become the dominant reproductive individuals. These are the gamergates, or "married workers," and their sex life can be brutal. In one species the gamergates venture outside of the nest to attract a male, engage him in copulation, then carry him into the nest before snipping off his genitals and throwing away the rest of his body. The severed genitals continue to inseminate the gamergate for up to an hour, after which they too are discarded."

I really wonder whether the argument from design would have survived a close acquaintance with the habits of insects around the world. This arrangement, at least, does not make the idea of a benevolent deity leap to mind.

December 09, 2008

Wonderful news from the New England Journal of Medicine (1, 2), summarized by FP Passport:

Results of the latest malaria vaccine trials will be published today in The New England Journal of Medicine, and from the looks of it, the news is good--fantastic, in fact. "We are closer than every before to having a malaria vaccine for use by children in Africa, says Christian Lucq, director of the PATH Malaria Vaccine Initiative.

First, some background: The new trials use a vaccine candidate known as RTSS, the most clinically advanced malaria vaccine in development. The two tests took place in Kenya and Tanzania, and included 340 and 894 children, respectively. After vaccination, children were visited in their homes to follow up on their health and most importantly, their contraction (or not) of malaria.

Here are some highlights from the results:

* Unlike previous trials, these studies administered the malaria vaccine in conjunction with the normal WHO schedule of vaccines like polio, MMR, and others. There was no interference on either side. That matters because if a malaria vaccine is every to be administered, it is likely to be administered in tandem with others.

* In infants of 8, 12, and 16 weeks, the vaccine reduced malaria infections by 65%.

* In children aged five to 17 months, the incidence of clinical malaria was reduced by 53%.

The results today set the stage for more Phase 3 trials--the last needed before lisencing of the vaccine. Future trials will continue to test safety, efficacy, and the possibility of a "booster" shot lengthening the already lengthy 18-month protection observed. 16,000 children will be involved in 11 sites found in 7 countries."

According to the CDC, malaria is the fourth leading cause of death among children under five. It kills at least a million people a year, and sickens hundreds of times that number. Besides the horrific burden of disease, death, and misery that malaria places on large chunks of the world, it also puts a serious economic burden on those countries where it's endemic -- which are, as it happens, often the countries that can least afford it.

So a malaria vaccine that's 50-65% effective would be a wonderful, wonderful thing.

September 12, 2007

"He knew his colors and shapes, he learned more than 100 English words, and with his own brand of one-liners he established himself in TV shows, scientific reports, and news articles as perhaps the world’s most famous talking bird.

But last week Alex, an African Grey parrot, died, apparently of natural causes, said Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard who studied and worked with the parrot for most of its life and published reports of his progress in scientific journals. The parrot was 31. (...)

When, in 1977, Dr. Pepperberg, then a doctoral student in chemistry at Harvard, bought Alex from a pet store, scientists had little expectation that any bird could learn to communicate with humans. Most of the research had been done in pigeons, and was not promising.

But by using novel methods of teaching, Dr. Pepperberg prompted Alex to learn about 150 words, which he could put into categories, and to count small numbers, as well as colors and shapes. “The work revolutionized the way we think of bird brains,” said Diana Reiss, a psychologist at Hunter College who works with dolphins and elephants. “That used to be a pejorative, but now we look at those brains — at least Alex’s — with some awe.” (...)

Alex showed surprising facility. For example, when shown a blue paper triangle, he could tell an experimenter what color the paper was, what shape it was, and — after touching it — what it was made of. He demonstrated off some of his skills on nature shows, including programs on the BBC and PBS. He famously shared scenes with the actor Alan Alda on the PBS series, “Look Who’s Talking.” (...)

Even up through last week, Alex was working with Dr. Pepperberg on compound words and hard-to-pronounce words. As she put him into his cage for the night last Thursday, Dr. Pepperberg said, Alex looked at her and said: “You be good, see you tomorrow. I love you.”"

I'm not sure the astonishing nature of Alex's language-learning comes through here. He could answer questions like 'What color?', 'What shape?' and 'What number?' Given a tray with blocks and balls of several different colors, he can say how many blocks of a given color there are -- separating them out from the blocks of a different color, and the balls of the same color. He can use and understand the word 'none'.

My favorite story about Alex comes from The Alex Studies, p. 147. Alex had been asked to identify the color and material of various objects, and apparently he got bored. (Who can blame him?) Here's what happened:

"In each of two additional trials (one on color, one on material), however, he did not respond correctly on the second try. He produced instead each of the wrong possible answers from the appropriate category, repeated each wrong answer, then grabbed the tray liner and tossed all the objects to the floor."

September 10, 2007

"Exploring the neurobiology of politics, scientists have found that liberals tolerate ambiguity and conflict better than conservatives because of how their brains work.

In a simple experiment being reported today in the journal Nature Neuroscience, scientists at New York University and UCLA show that political orientation is related to differences in how the brain processes information.

Previous psychological studies have found that conservatives tend to be more structured and persistent in their judgments whereas liberals are more open to new experiences. The latest study found those traits are not confined to political situations but also influence everyday decisions.

The results show "there are two cognitive styles -- a liberal style and a conservative style," said UCLA neurologist Dr. Marco Iacoboni, who was not connected to the latest research.

Participants were college students whose politics ranged from "very liberal" to "very conservative." Scientists instructed them to tap a keyboard when an M appeared on a computer monitor and to refrain from tapping when they saw a W.

M appeared four times more frequently than W, conditioning participants to press a key in knee-jerk fashion whenever they saw a letter.

Each participant was wired to an electroencephalograph that recorded activity in the anterior cingulate cortex, the part of the brain that detects conflicts between a habitual tendency (pressing a key) and a more appropriate response (not pressing the key). Liberals had more brain activity and made fewer mistakes than conservatives when they saw a W, researchers said. Liberals and conservatives were equally accurate in recognizing M. (...)

Frank J. Sulloway, a researcher at UC Berkeley's Institute of Personality and Social Research who was not connected to the study, said results "provided an elegant demonstration that individual differences on a conservative-liberal dimension are strongly related to brain activity."

Analyzing the data, Sulloway said liberals were 4.9 times as likely as conservatives to show activity in the brain circuits that deal with conflicts, and 2.2 times as likely to score in the top half of the distribution for accuracy."

It's a good thing I'm noting this without comment. Otherwise, I might have had to say something like: liberals are better at dealing with complexity, and at responding to the unexpected; and besides, we're over twice as likely to get things right! Hah!

May 31, 2007

Yesterday, John Quiggin had a post on Crooked Timber that was very interesting. It concerns an idea I had been rather vaguely aware of, but hadn't really focussed in on: that Rachel Carson and the environmentalist movement were responsible for the deaths of thousands, maybe millions, even "tens of millions" from malaria. This is completely untrue (I'll say why below the fold), not that that has stopped people from saying that it is in places like the WSJ, the National Review Online, and even the US Senate.

As Quiggin notes, there's a mystery about this, namely: where did it come from? It has all the hallmarks of a coordinated campaign -- editorials placed in prominent newspapers, all citing the same dubious examples, for instance, and its very own website -- but it's not clear why anyone would undertake such a campaign.

"One of the great puzzles of the DDT myth has been that it appeared to arise from pure ideological animus against Carson and the environmental movement – DDT is not patented so there were no profits to be obtained from pushing it."

So what's up?

Well: I had started to try to piece the story together when I discovered that Tim Lambert had done it for me. So I'll just quote him (though you should read the whole thing):

"So how did the "Rachel killed millions" claim get from lunatic fringe to mainstream?

Well, in 1998, the new Director-General of the World Health Organization, Gro Harlem Brundtland established the Tobacco Free Initiative to reduce death and disease caused by tobacco use. Since it would also reduce tobacco company profits, they used one of their favourite tactics: When an agency plans to take actions against smoking, tobacco companies pay third parties to attack the agency for addressing tobacco instead of some other issue. For example, when the FDA proposed to regulate nicotine, Philip Morris organized and paid for an expensive anti-FDA campaign of radio, television and print ads from think tanks such as the CEI.

So Philip Morris hiredRoger Bate to set up a new astroturf group Africa Fighting Malaria and criticize the WHO for not doing enough to fight malaria. The key elements of AFM's strategy:

"Simplify our arguments.
Pick issues on which we can divide our opponents and win. Make our case on our terms, not on the terms of our opponents - malaria prevention is a good example. ...
this will create tensions between LDCs and OECD countries and between public health and environment."

The simple argument they used to drive a wedge between public health and environment was that we had to choose between birds and people. That by banning DDT to protect birds, environmentalists caused many people to die from malaria."

So, in a nutshell: the WHO was about to undertake an initiative that would have harmed the tobacco companies. The tobacco companies, in turn, hired shills to attack the WHO. They presumably hired some to attack the WHO's tobacco initiative, but they also hired people to attack other things the WHO was doing in order to discredit it more generally. Thus, the attack on Rachel Carson.

***

Malaria prevention is incredibly important. For that matter, so is the WHO and its anti-tobacco initiative. This story shows the tobacco industry funding people to spread misinformation, not because they themselves have any interest in malaria and DDT, but just to sow confusion and skepticism about the WHO at a time when it was a threat to their interests.

This is a story of intellectual corruption. And it has real public costs. People need to be able to trust experts: the alternative is everyone having to develop his or her own expertise in everything. When people who should know better allow themselves to be paid to shill for industry, they undermine that trust. And that makes us all worse off.

February 22, 2007

"Chimpanzees living in the West African savannah have been observed fashioning deadly spears from sticks and using the hand-crafted tools to hunt small mammals -- the first routine production of deadly weapons ever observed in animals other than humans.

The multi-step spear-making practice, documented by researchers in Senegal who spent years gaining the chimpanzees' trust, adds credence to the idea that human forebears fashioned similar tools millions of years ago.

The landmark observation also supports the long-debated proposition that females -- the main makers and users of spears among the Senegalese chimps -- tend to be the innovators and creative problem solvers in primate culture.

Using their hands and teeth, the chimpanzees were repeatedly seen tearing the side branches off long straight sticks, peeling back the bark and sharpening one end, the researchers report in today's on-line issue of the journal Current Biology. Then, grasping the weapon in a "power grip," they jabbed into tree-branch hollows where bush babies -- small monkey-like mammals -- sleep during the day.

After stabbing their prey repeatedly, they removed the injured or dead animal and ate it.

"It was really alarming how forceful it was," said lead researcher Jill D. Pruetz of Iowa State University in Ames, adding that it reminded her of the murderous shower scene in the Alfred Hitchcock movie "Psycho." "It was kind of scary." (...)

In a typical sequence, the animal first discovered a deep hollow suitable for bush babies, which are nocturnal and weigh about half a pound. Then the chimp would break off a nearby branch -- on average about two feet long, but up to twice that length -- trim it, sharpen it with its teeth, and poke it repeatedly into the hollow at a rate of about one or two jabs per second.

After every few jabs, the chimpanzee would sniff or lick the tip, as though testing to see if it had "caught" anything."

Though I don't really have anything to say about it, I was intrigued by the part about female chimpanzees being the more proficient tool-makers and problem-solvers:

"Adrienne Zihlman, an anthropologist at the University of California at Santa Cruz, said the work supports other evidence that female chimps are more likely to use tools than males, are more proficient tool users, and are crucial to passing that cultural knowledge to others.

"Females are the teachers," Zihlman said, noting that juvenile chimps in Senegal were repeatedly seen watching their mothers make and hunt with spears.

"They are efficient and innovative, they are problem solvers, they are curious," Zihlman said of females. And that makes sense, she said.

"They are pregnant or lactating or carrying a kid for most of their life," she said. "And they're supposed to be running around in the trees chasing prey?""

I think primatology is one of the coolest disciplines in the world. I only hope it has a chance to continue -- most primate species, chimps included, are projected to go extinct within a few decades.

January 08, 2007

"A type of cell that floats freely in the amniotic fluid of pregnant women has been found to have many of the same traits as embryonic stem cells, including an ability to grow into brain, muscle and other tissues that could be used to treat a variety of diseases, scientists reported yesterday.

The cells, shed by the developing fetus and easily retrieved during routine prenatal testing, are easier to maintain in laboratory dishes than embryonic stem cells -- the highly versatile cells that come from destroyed human embryos and are at the center of a heated congressional debate that will resume this week.

Moreover, because the cells are a genetic match to the developing fetus, tissues grown from them in the laboratory will not be rejected if they are used to treat birth defects in that newborn, researchers said. Alternatively, the cells could be frozen, providing a personalized tissue bank for use later in life. (...)

"They grow fast, as fast as embryonic stem cells, and they show great pluripotentiality," meaning they can become many kinds of tissues, said study leader Anthony Atala, director of the Institute for Regenerative Medicine at Wake Forest University School of Medicine in Winston-Salem, N.C. "But they remain stable for years without forming tumors," he added, something that embryonic cells are not very good at.

Atala and other scientists emphasized that they don't believe the cells will make embryonic stem cells irrelevant.

"There's not going to be one shoe that fits all," said Robert Lanza, scientific director at Advanced Cell Technology in Worcester, Mass. "We're going to have to see which ones are most useful for which clinical conditions."

George Daley, a Harvard stem cell researcher, echoed that sentiment. "They are not a replacement for embryonic stem cells," he said. (...)

In the laboratory, the amniotic cells can mature into all of the major types of cells, dividing at the impressive clip of once every 36 hours yet never showing signs of aging and never becoming tumors -- even after living for more than two years in the lab.

With co-workers from Wake Forest and from Children's Hospital in Boston, Atala coaxed the cells to become brain cells and injected them into the skulls of mice with diseased brains. The new cells filled in diseased areas and appeared to make new connections with nearby healthy neurons.

When coaxed to become bone cells and seeded onto a gelatin scaffold that was then implanted in a mouse, the cells calcified and turned into dense, healthy bone.

Under other conditions they became muscle, fat, blood vessel and liver cells.

Atala said that if 100,000 women donated their amniotic cells to a bank, that would provide enough cells of sufficient genetic diversity to provide immunologically compatible tissues for virtually everyone in the United States. With more than 4 million U.S. births a year, it would not take long to collect that many specimens, he said -- especially because the cells can be found not only in amniotic fluid but also in the placenta, which is discarded after birth."

If this works out -- and, needless to say, that's a big if -- it would be wonderful news. This isn't just because it would be a source of stem cells that have some of the properties of embryonic stem cells but don't require the destruction of embryos. It's also important that its source -- amniotic fluid -- is so readily available, and from so many different kinds of people. Embryonic stem cells derived from excess IVF embryos are only as diverse as couples seeking IVF, and there have been a lot of questions both about how diverse in all the usual ways those couples are, and also about what the fact that they all have one thing in common -- infertility -- means for the resulting stem cell lines. By contrast, pretty much everyone has babies. Moreover, taking samples of amniotic fluid is something a lot of people do anyways, and since amniocentesis is often beneficial and desirable for prospective parents, if it turns out that some group can't afford it, members of that group might be happy to voluntarily undergo amniocentesis in exchange for the right to derive stem cells from the amniotic fluid.

One of the moral questions raised by the prospect of stem cell therapies is: if we were to design a bank of stem cells, what lines would it include? Stem cells, like organs, have to be a good enough genetic match for the person they will be transplanted into. If a stem cell bank included the lines that would match the greatest number of people, then in the USA and Europe, it would turn out, in practice, that the vast majority of people who could get a good match would be white. If, on the other hand, we tried to provide good matches for roughly equal percentages of all ethnic groups, then the bank would be able to help fewer people. (I discuss this question here.)

This problem exists in part because the range of embryonic stem cell lines available from IVF embryos is limited, and deriving embryonic stem cells using somatic cell nuclear transfer is difficult, and likely to be quite expensive. (It also involves women donating eggs -- not, I am told, a pleasant process.) As Atala says, If we can derive stem cell lines from amniotic fluid, and if those lines can do some of the work that embryonic stem cells do, then we would have a vast, cheap and diverse source of useful stem cells. That would mean that we could construct a larger bank, and thus that the problem of the banks genetic diversity would be a lot more tractable -- at least for those diseases that could be treated by these cells.

However, as Robert Lanza said in the Post article, "There's not going to be one shoe that fits all (...) We're going to have to see which ones are most useful for which clinical conditions." -- If there's one thing I wish that everyone understood about stem cells, it's that they are not all the same. Adult stem cells are extremely different from embryonic stem cells, and if this research holds up, these new stem cells will undoubtedly be different from both. (Moreover, different lines of stem cells differ from one another -- they are not at all interchangeable.) There may be some diseases that amniotic stem cells can be used to treat; there will probably be some that still require embryonic stem cells.

Moreover, there's one thing that this research does not suggest we might use these amniotic stem cells to replace. Unfortunately, that's somatic cell nuclear transfer. SCNT promises to be extraordinarily useful for research, for reasons I detailed here. (Scroll down until you see a paragraph beginning 'The Main Issue', in bold.) Absent some reason to think that we could use amniotic cells not just to derive stem cell lines, but to do something very much like cloning, this won't replace SCNT.

December 07, 2006

"The issue of whether the toilet seat should be left up or down after use seemingly generates a lot of passion among the parties concerned, however, scientific inquiries into the matter are almost non-existent. Notable exceptions are Choi (2002) and Harter (2005). Choi (2002) argues that the rule of leaving the toilet seat down after use is inefficient in the sense that there is at least one other rule that outperform this rule. The unit of analysis in Choi (2002) is the household and the efficient rule is defined as one that minimizes the total cost of toilet seat operations per household. Choi (2002) does not model the issue as a situation of conflict, hence ignores the game theoretic aspects of the problem. Harter (2005) models the situation as a cooperative game and proposes a contract that splits the costs of toilet seat operations evenly among the parties. Both papers agree that the social norm of leaving the toilet seat down in inefficient in the sense that it does not minimize the total cost of toilet seat operations per household. However, both papers fail to address an important concern: If a female finds the toilet seat in a wrong position then she will most probably yell at the male involved. This yelling inflicts a cost on the male. Based on this omission, women may argue that the analysis in these papers is suspect.

In this paper, we internalize the cost of yelling and model the conflict as a non-cooperative game between two species, males and females. We find that the social norm of leaving the toilet seat down is inefficient. However, to our dismay, we also find that the social norm of always leaving the toilet seat down after use is not only a Nash equilibrium in pure strategies but is also trembling-hand perfect. So, we can complain all we like, but this norm is not likely to go away."

From the body of the study:

"Assume that the inconvenience cost of changing the seat position is C. Further assume that the need for #1 arises with a probability p. Let’s look at the average costs to John and Marsha:

The average cost to John as a bachelor

Doing #1 this time when he did #2 last time + Doing #2 this time when he did #1 last time = p x (1 x p) x C+ (1 x p) x p x C= 2 x p x (1 x p) x C (1)

The average cost to Marsha as a bachelorette

Obviously 0 since she performs everything with the seat in the down position."

There are lots more equations where those came from.

Back in grad school, I decided that there were two vital facts that philosophers needed to engrave in their minds and recall on a regular basis:

(1) Occasionally, Wittgenstein was wrong

(2) There are some situations to which game theory cannot usefully be applied.

I leave it to the reader to decide which bears most directly on the matter at hand.